You could probably do an invisible weapon that is fired when the unit infiltrates the command center and will knock out power like the microwave weapon. I don't know how to specifically target defenses though.
I haven't used the infiltrator much so I don't remember all the effects he has.
You'd better use the SUBDUAL_BUILDING code for this (and remove it from the Micro Tank). I made a Radar Jammer using this method, I gave the radar its own armour type, and SUBDUAL_BUILDING has 0% against all others. So with FireWeaponUpdate and a weapon with a very big DamageRadius, the jammer automatically disables any enemy radar it comes near.